예제 #1
0
    default=sys.stdout)
args = parser.parse_args()

# First get the lineage (and fail now if not found)
lineage = get_lineage(args.species, args.email)
if not lineage:
    raise RuntimeError(
        "Could not find lineage information on NCBI for species '%s'" %
        args.species)

print('Found lineage: %s' % lineage)

# Prepare the bibliographic reference
ref = Reference()
if args.ref_pubmed_id:
    ref.pubmed_id = args.ref_pubmed_id
if args.ref_consortium:
    ref.consrtm = args.ref_consortium
if args.ref_authors:
    ref.authors = args.ref_authors
if args.ref_title:
    ref.title = args.ref_title
if args.ref_journal:
    ref.journal = args.ref_journal
else:
    now = datetime.datetime.now()
    ref_date = now.strftime("%m-%b-%Y").upper()
    # Temp switch to C to get english month abbr
    saved = locale.setlocale(locale.LC_TIME)
    try:
        locale.setlocale(locale.LC_TIME, "C")
예제 #2
0
                print(gb, f)

        # sort features by start location, source always first
        gb.features.sort(key=lambda f: (-len(gb.seq)) *
                         (f.type == "source") + f.location.start)

        # translate color from notes to ApEinfo
        for feature in gb.features:
            translate_color(feature)

        # Add an EcoFlex article reference
        ref = Reference()
        ref.authors = 'Moore SJ, Lai HE, Kelwick RJ, Chee SM, Bell DJ, Polizzi KM, Freemont PS.'
        ref.title = 'EcoFlex: A Multifunctional MoClo Kit for E. coli Synthetic Biology.'
        ref.journal = 'ACS Synth Biol 2016;5:1059-1069.'
        ref.pubmed_id = '27096716'
        gb.annotations['references'].append(ref)

        # Fix the direct submission reference
        ref = Reference()
        # ref = gb.annotations["references"][-1]
        ref.authors = "Larralde M"
        ref.title = "Direct Submission"
        ref.journal = "Distributed with the MoClo Python library\nhttps://github.com/althonos/moclo"
        gb.annotations['references'].append(ref)

        # write the final record
        dst_dir = os.path.abspath(
            os.path.join(__file__, "..", "..", "moclo-ecoflex", "registry",
                         "ecoflex"))
        dst_file = os.path.join(dst_dir, "{}.gb").format(info["id"])